title: Genome wide-binding profile of tethered Nrf2-MafG (T-N2G) heterodimers in the small Maf-deficient cells [ChIP-seq]

status: Public on Aug 06 2019

city: Aoba-ku, Sendai

first: Fumiki

last: Katsuoka

state: Miyagi

address: 2-1 Seiryo-cho

institute: Tohoku University

summary: To elucidate the function of Nrf2-small Maf heterodimer, we constructed a tethered Nrf2-MafG (T-N2G) heterodimer using a flexible linker peptide and examined its function in the small Maf-deficient mouse embryonic fibroblast (MEF).

overall_design: ChIP-seq was performed using anti-MafG antibody on chromatin extracted from the T-N2G-expressing MafF-/-::MafG-/-::MafK-/- (F0G0K0) MEFs, treated with 100µM Diethyl Maleate (DEM) or Vehcle for 4hr.

first: Akihito

last: Otsuki

first: Mizue

last: Takahashi

first: Shin

last: Ito

first: Masayuki

last: Yamamoto


title: Epigenomic and transcriptomic analysis of bone marrow LSK cells in WT, G12D, Ezh2-KO, and G12D with Ezh2-KO mice

status: Public on Jun 17 2019

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

country: USA

institute: St. Jude Children's Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Gene expression profile in the tethered Nrf2-MafG (T-N2G) heterodimer-expressing small Maf-deficient cells [RNA-seq]

country: Japan

overall_design:
polyA RNA-seq was performed using RNA from Immortalized MafF-/-::MafG-/-::MafK-/- (F0G0K0) MEFs and T-N2G-expressing F0G0K0 MEFs, treated with 100µM Diethyl Maleate (DEM) or Vehcle for 12hr.

sample title - condition - replicate (in the genes.read_group_tracking.txt)
2_Mock_Veh - Mock_Veh - 1
1_Mock_Veh - Mock_Veh - 0
3_Mock_Veh - Mock_Veh - 2
2_Mock_DEM - Mock_DEM - 1
1_Mock_DEM - Mock_DEM - 0
3_Mock_DEM - Mock_DEM - 2
3_T-N2G_Veh - N2_Veh - 2
1_T-N2G_Veh - N2_Veh - 0
2_T-N2G_Veh - N2_Veh - 1
1_T-N2G_DEM - N2_DEM - 0
2_T-N2G_DEM - N2_DEM - 1
3_T-N2G_DEM - N2_DEM - 2


title: Phenotypic and Functional Characteristics of Human Schwann Cells as Revealed by Cell-Based Assays and RNA-SEQ

status: Public on Jul 03 2019

city: Provo

first: David

middle: Wayne

last: Sant

state: UT

address: 1712 South East Bay Blvd, Building 5 Suite 300

department: Biomedical Informatics

institute: Noorda College of Osteopathic Medic

summary: In this study we show the inherent differences between human and rat Schwann cells.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Human and rat schwann cells cultured until passage 2

first: Paula

last: Monje

first: Gaofeng

last: Wang


status: Public on Apr 26 2019

city: Taipei

first: Po-Chen

last: Hsu

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: To understand the Sef1-dependent gene expression in Lachancea kluyveri under both fermentative and respiratory conditions, we perfomred the genome-wide gene expression profiling for the log-phase cells of Lachancea kluyveri wild type and sef1 deletion mutant under both YPD and YPGly conditions.

overall_design: Cells fom overnight YPD cultures were diluted into YPD and YPGly at a cell density of 0.2 OD per ml and incubated at 30°C fro 5.5 h.  Four biological replicates fro each strain under each condition were preprared.

first: Jun-Yi

last: Leu


title: The Proteogenomic Landscape of Curable Prostate Cancer [microarray]

status: Public on Jun 30 2019

city: Toronto

first: Yu-Jia

last: Shiah

state: Ontario

address: MaRS Centre 661 University Avenue Suite 510

department: Informatics and Bio-computing

country: Canada

institute: Ontario Institute for Cancer Research

summary: DNA sequencing studies have identified specific recurrent somatic mutations that drive the aggressiveness of localized prostate cancers. Surprisingly, though, it is poorly understood how the prostate cancer proteome is shaped by genomic, epigenomic and transcriptomic dysregulation. To fill this gap, we profiled the whole genomes, methylomes, epigenomes, transcriptomes and proteomes of 55 localized, intermediate-risk, prostate cancers. This multi-modal dataset revealed that the genomic subtypes of prostate cancer converge on four proteomic subtypes, which are associated with distinct clinical trajectories. ETS fusion genes, the most common mutation in prostate tumours, perturb the proteome and transcriptome in divergent ways – with different genes and pathways affected at each level. Indeed, mRNA abundance changes explain only ~10% of variability in protein levels. Perhaps as a direct result, prognostic biomarkers that combine genomic or epigenomic features with proteomic ones significantly outperform those comprised of either molecular feature alone. These data suggest that the proteome of prostate cancer is shaped by a complex interplay of genomic, epigenomic, transcriptomic and post-transcriptional dysregulation.

overall_design:
In total we have 214 samples (213 unique samples) accross 5 different batches. Batch 1, 3, 4 and 5 are based on the HuGene2.0 platfrom whereas batch 2 is based on HTA2.0 platform

Please note that CPCG0398_rep is a technical replicate of CPCG0398, therefore the CPCG0398 column in the Matrix_processed_data.tsv represents the average of the original CPCG0398 and the CPCG0398_rep.

first: Paul

middle: C

last: Boutros


title: Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits

status: Public on Jun 24 2019

city: Wuhan

first: xuewen

last: xu

state: Hubei

address: Shizishan street, No.1

country: China

institute: Huazhong Agricultural University

summary: Genetic analysis of gene expression level is a promising approach for characterizing candidate genes that are involved in complex economic traits such as meat quality. In the present study, we conducted expression quantitative trait loci (eQTL) and allele-specific expression (ASE) analyses based on RNA-sequencing (RNAseq) data from the longissimus muscle of 189 Duroc × Luchuan crossed pigs in order to identify some candidate genes for meat quality traits. Using a genome-wide association study based on a fixed linear model, we identified 7,192 cis-eQTL corresponding to 2,098 cis-genes (p ≤ 1.33e-3, FDR ≤ 0.05) and 6,400 trans-eQTL corresponding to 863 trans-genes (p ≤ 1.13e-6, FDR ≤ 0.05). ASE analysis using RNAseq SNPs identified 9,815 significant ASE-SNPs in 2,253 unique genes. Integrative analysis between the cis-eQTL and ASE target genes identified 540 common genes, including 33 genes with expression levels that were correlated with at least one meat quality trait. Among these 540 common genes, 63 have been reported previously as candidate genes for meat quality traits, such as PHKG1 (q-value = 1.67e-6 for the leading SNP in the cis-eQTL analysis), NUDT7 (q-value = 5.67e-13), FADS2 (q-value = 8.44e-5), and DGAT2 (q-value = 1.24e-3).This study provides valuable information on the genetics of gene expression in porcine skeletal muscle. The characterized cis-genes and ASE genes, combined with the correlations between gene expression level and meat quality traits will be useful to prioritize candidate genes in further studies.

overall_design: Transcriptome sequencing in longissimus dorsi muscle of 189 pigs from the crossing of 8 Duroc boars and 158 Luchuan sows.

first: Xuewen


title: Transcriptomic profiles of jejunum in piglets exposed to Fumonisin B1

status: Public on Apr 15 2019

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

department: GeT-TRiX facility

country: France

institute: INRAE

summary: Fumonisin B1 (FB1) is a mycotoxin produced by Fusarium species. In mammals, this toxin causes multiple organ-specific damages. Among its multiple effects, FB1 promotes hepatotoxicity, is immunotoxic and alters the intestinal functions. Despite its inhibitory effect on de novo ceramide synthesis, the molecular mechanism of FB1 action and toxicity remain unclears. In order to explore the mechanism of FB1 toxicity, we analyzed the transcriptome of the jejunal section which is targeted by FB1.

overall_design: Ten weeks old pigs were sacrificed after 4 weeks feeding with control diet (6 pigs) or feeding with control diet artificially contaminated with 10 ppm Fumonisin B1 (6 pigs). After sacrifice Jejunal section samples from each of 12 pigs are collected and used for microarray gene expression study.

first: Nicolas

last: Loiseau

first: Pascal

last: Gourbeyre

first: Joëlle

last: Laffitte

first: Julien

last: Fayet

first: Anne-Marie

last: Cossalter

first: Philippe

last: Pinton

first: Isabelle

last: Oswald


title: RNA-Seq Analysis of Changes in Human Myometrial Tissue mRNA Expression Upon Labour Onset and Progression in Term Pregnancy

status: Public on Apr 23 2019

city: london

first: kaiyu

last: lei

state: London

address: ducan road

department: Surgery and Cancer

country: United Kingdom

institute: imperial college london

summary:
Purpose: The cause of labour initiation has yet to be fully elucidated for human pregnancy. This has hindered attempts to find effective therapies for the prevention of preterm labour, which affects up to 10% of pregnancies in the UK and it is the most dominant cause of perinatal death (75% of all cases). The myometrium of the uterus is where contractions that characterise labour take place, and it is here where changes at the molecular level responsible for triggering labour potential originate from. We used RNA-Seq-based mRNA sequencing technology in an attempt to identify mRNA transcripts that are differentially expressed in the myometrium upon the onset of labour, by comparing the expression profiles of tissues samples that represented non-labour (TNL), early labour (TEaL, ≤ 3 cm cervical dilation) and established labour (TEsL, > 3 cm cervical dilation) states at term (> 37 weeks gestation) pregnancy.
Methods: Myometrial biopsies from women undergoing Caesarean section were collected in accordance with the Declaration of Helsinki guidelines, and with approval from the local research ethics committee for Chelsea & Westminster Hospital (London, UK; Ethics No. 10/H0801/45). Informed written consent was obtained from all women who participated. Biopsies were excised from the upper margin of the incision made in the lower segment of the uterus, immediately washed with Dulbecco's phosphate-buffered saline (Sigma) and dissected into pieces approximately measuring 2-3 mm3. For RNA study, biopsies were immersed in RNAlater (Sigma) within 6 minutes after biopsy excision from the uterus and stored at 4°c overnight, before being taken out of RNAlater solution to be frozen for long-term storage at -80°c. For CHIP study, biopsies were snap-frozen in liquid nitrogen and stored at -80°c. All specimens were categorised into four groups according to their labour stages: preterm not in labour (PTNL, n=6), term not in labour (TNL, n=8), term in early labour (TEaL, defined as cervical dilatation <3 cm, n=8) and term in established labour (TEsL, defined as cervical dilatation >3 cm, n=6). For each sample, 60-100 mg of myometrium tissue were extracted in TRIzol (Life Technologies) by mechanical homogenisation in a Precellys 24 bead-based homogeniser using 5 cycles of 5000 rpm for 20 seconds, before chloroform treatment and centrifugation at 4°c. RNA was extracted from the aqueous phase of centrifuged homogenates using the TRIzol Plus RNA Purification kit (Life Technologies) with on-column DNase treatment prior to elution, all according to manufacturer's instructions. Final RNA samples were stored at -80°c. The quantity and quality RNA was measured using a Nanodrop ND-1000 spectrophotometer (LabTech),  Qubit fluorimeter (Life Technologies) and Bioanalyser 2100 (Agilent Technologies). Preparation of cDNA libraries was carried out using the TruSeq Stranded mRNA Sample Preparation kit (Illumina), following the high-throughput sample (HT) protocol. The quantity and quality of cDNA libraries were also tested by a Qubit fluorimeter and Bioanalyser 2100. TruSeq Stranded libraries were then multiplexed and sequenced with the average of 42 million DNA fragments per sample (100 bp paired-end reads). Quality control was performed using FastQC software (version 0.11.2). RNA-Seq reads was aligned to the GRCh38 Homo sapiens reference genome downloaded from Ensembl (release 81) with HISAT version 2.0.1 using parameters of --known-splicesite-infile --dta-cufflinks --rna-strandness RF --phred33 –p 4 -q. A list of known splice sites generated from the Ensembl GTF file using an accessory python script included in the HISAT2 package was provided to --known-splicesite-infile, of which HISAT2 will make use to assist the alignment of reads spanning two or more exons. Ensembl annotated a total of 65,989 genes, which includes 20,276 protein coding genes. As one human gene usually contains multiple transcript models, we thus conducted a transcript merging procedure to produce gene level models for expression analysis. Specifically, exons labeled as ‘retained_intron’ were first excluded, then overlapping interval exons of each gene were merged and a final gene level model was produced in GFF format. Only uniquely mapped (i.e. reads with the tag of NH:i:1) reads were used to produce gene read counts and calculate gene expression levels. The raw read count matrix was normalised with DESeq2 (version 1.6.3). Expression level of each gene in each sample was represented as RPKM (reads per kilobase per million mapped reads). Differentially expressed genes (DEGs) between two groups of samples were identified with DESeq2 (version 1.6.3), edgeR (version 3.8.6) and Cuffdiff (version 2.2.1). For DESeq2 and edgeR, we used the normalised read count matrix as input, and for Cuffdiff, we used the alignment bam files with uniquely mapped reads as input. Raw p-values were adjusted by FDR to produce q-values, and q-value of 0.05 were chosen as the cut-off for statistical significance in DESeq2, edgeR as well as Cuffdiff.
Results: 22 RNA samples from three different labour groups were sequenced and an average of 53 million reads were obtained from each sample. More than 97.34% of reads were successfully aligned to GRCh38 reference human genome and the unique concordant pair ratio was greater than 92.39%. In total, 60,593 genes were mapped with the following criteria: (1) at least one RNA-seq read assigned to a gene; (2) we only assign a read to a gene when > 90% of this read falls into the exon regions of this gene. The principal component analysis (PCA) of these 22 samples showed that TNL and TEsL samples formed two distinct clusters whereas the TEaL group featured relatively great internal differences. Nevertheless, half of the samples from TEaL group was clustered with the TNL group and the other half was more separated yet closer to two samples of TEsL group. To determine the transcripts associated with labour, three software packages (DESeq2, EdgeR and Cuffdiff) were used to perform differential expression The transcript with a q value <0.05 in at least two methods was defined as a shared differentially expressed gene (DEG). As a result, 132 and 399 genes were identified comparing TNL with TEaL and TEsL, respectively, whereas no gene was significantly differentially expressed between TEaL and TEsL groups. Due to big differences among individual samples, in this study, the expression fold change (FC) was calculated as the ratio of median reads per kilobase per million mapped reads (RPKMs) with the bigger median RPKM divided by the smaller median RPKM. In order to minimise the noise derived from genes with low expression but high FC, we further filtered gene lists according to the following rational: if the original value of any median RPKM was <1, we artificially turned it into 1 before calculating the FC. Finally, two robust gene lists with an expression FC >1.5 between two groups (TNL vs. TEaL and TNL vs. TEsL) were generated containing 70 and 232 DEGs, respectively.
Conclusions: This study, for the first time,  identifies differentially expressed genes (DEGs) and pathways that are involved in the myometrial transition from non-labouring to labouring phenotype by using samples from different stages of pregnancy and labour. The DEG lists are generated by subjecting the raw data to three sofware packages (DESeq2, edgeR and Cuffdiff), which makes the yield DEGs more robust. We conclude that some early responsive genes in circadian clock and inflammation pathways are likely to account for the labour onset and no significant changes are found on the transcription level once the labour starts.

overall_design: Comparisons made between no labour (TNL, n = 8), early labour (TEaL, n = 8) and established labour (TEsL, n = 6) lower segment myometrial tissue samples, which were collected during Caesarean section (CS) with informed written consent

first: Kaiyu

last: Lei

first: Pei

middle: F

last: Lai

first: Xiaoyu

last: Zhan

first: Qiye

last: Li

first: Guojie

last: Zhang

first: Anna

last: Zekavati

first: Michael

last: Mueller

first: Mark

middle: R

last: Johnson


title: ATAC-seq analysis in bone marrow LSK cells in WT, G12D, Ezh2-KO and G12D with Ezh2-KO (G12D_Ezh2-KO) mice

first: Jian

last: Xu

summary: Epigenetic gene regulation and metabolism are highly intertwined, yet little is known whether and how altered epigenetics influences cellular metabolism in cancer progression. Here we show that EZH2 and NRasG12D mutations cooperatively induce progression of myeloproliferative neoplasms to fully penetrant, transplantable and lethal myeloid leukemias in mouse. EZH1, an EZH2 homolog, is indispensable for EZH2-deficient leukemia-initiating cells (LICs) and constitutes an epigenetic vulnerability. BCAT1, the first enzyme catalyzing transamination of branched-chain amino acids (BCAAs), is repressed by EZH2 in normal hematopoiesis and aberrantly activated in EZH2-deficient myeloid neoplasms in mouse and human. Enhanced BCAT1 promotes BCAA production in LICs ex vivo and in vivo, resulting in activated mTOR signaling. Genetic and pharmacological inhibition of BCAT1 selectively impairs EZH2-deficient LICs and constitutes a metabolic vulnerability. These findings establish an example how epigenetic alterations modify metabolic adaptation in myeloid transformation and provide a rationale for targeting the epigenetic and metabolic liabilities of cancer-initiating cells.

overall_design: ATAC-seq was performed to determine the chromatin accessibility in bone marrow LSK cells from WT, G12D, Ezh2-KO and G12D with Ezh2-KO (G12D_Ezh2-KO) mice

first: Zhimin

last: Gu

first: Yuxuan

last: Liu


title: CBFβ-MYH11 fusion blocks hematopoietic differentiation via repression of a GATA2 gene program

status: Public on Mar 22 2019

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

department: RIMLS

country: Netherlands

institute: Radboud University

summary: The CBFβ-MYH11 fusion generated by inv(16) aberration is proposed to block normal myeloid differentiation, but whether this subtype of leukemia cells is poised for an unique cell lineage remains unclear. Here, we surveyed the functional consequences of CBFβ-MYH11 in inv(16) patient blasts and two inducible systems by multi-omics profiling. The primary inv(16) cells stay closer with megakaryocyte and erythrocyte lineages along the cell differentiation trajectory, and share common transcriptomic signatures and epigenetic determiners. Using in vitro differentiation systems, we reveal that CBFβ-MYH11 knockdown establishes normal endomitosis-related processes, which are crucial for megakaryocyte maturation. Two pivotal regulators, GATA2 and KLF1, are identified to complementally occupy RUNX1 binding sites upon the fusion protein knockdown. Overexpression of GATA2 partly restores megakaryocyte directed differentiation suppressed by CBFβ-MYH11, and additional factors like KLF1 and EGR1 might be required to coordinately prevent CFB-MYH11 leukemogenesis. Together, our findings suggest that in inv(16) leukemia, the CBFβ-MYH11 fusion inhibits primed megakaryopoiesis by interfering with a balanced transcriptional program involving GATA2 and KLF1.

overall_design: ChIP-seq and RNA-seq using an AML cell line harbouring a dox inducible CBFB-MYH11 knockdown construct (induction using 600 ng/ml dox for 72 hours)

first: Guoqiang

last: Yi

first: Amit

last: Mandoli

first: Laura

last: Jussen

first: Esther

last: Tijchon

first: Bowon

last: Kim

first: Gaelle

last: Cordonnier

first: Jonathan

last: Bond


title: ChIP-seq analysis of H3K4me3,H3K27ac and H3K27me3 in bone marrow LSK cells in WT, G12D, Ezh2-KO and G12D with Ezh2-KO (G12D_Ezh2-KO) mice

overall_design: ChIP-seq was performed to determine the chromatin occupancy of histone marks H3K4me3,H3K27ac and H3K27me3 in WT, G12D, Ezh2-KO and G12D with Ezh2-KO (G12D_Ezh2-KO) mice


title: Dynamic behavior of the epigenetic machinery upon thermal stress

status: Public on May 31 2019

summary: Maintenance of the epigenome is of utmost importance to warrant appropriate cellular functioning Here we analyzed PRC1/2 function, in response to cellular stress. We observe that heat shock (HS) leads to nucleolar accumulation of CBX proteins, and are strongly immobilized in a 1,6-hexanediol insensitive manner, suggestive of a HS-induced liquid-to-solid phase transition of the nucleolus. CBX protein recovery from the nucleolus is dependent on heat shock protein (HSP) activity. LC-MS/MS analyses of nucleoli shows HS-induced nucleolar accumulation of PRC1/2 subunits, various chromatin regulators, HSPs, and the 26S proteasome. Finally, we find that HS leads to a strong reduction of PRC1/2 chromatin binding at target genes and loss of H2AK119ub and H3K27me3. Our findings demonstrate that thermal stress results in a rapid accumulation of epigenetic regulators in the nucleolus, and a concomitant loss of PRC1/2 complex chromatin binding and associated epimarks, underlining that environmental stress directly alters the epigenome.

overall_design: ChIP-seq analysis of CBX proteins using control and Heatshock induced cells was performed using illumina high-throughput sequencing

first: Maria

last: Azkanaz

first: Aida

last: López

first: Bauke

last: de Boer

first: Pierre-Olivier

last: Angrand

first: Edo

last: Vellenga

first: Harm

middle: H

last: Kampinga

first: Steven

last: Bergink

first: Jan

middle: J

last: Schuringa

first: Vincent

last: van den Boom


title: E-cadherin loss induces autocrine activation of oncogenic growth factor signalling in metastatic lobular breast cancer.

first: Joost

last: Martens

summary:
Background: Despite the fact that loss of E-cadherin is causal to the development and progression of invasive lobular breast cancer (ILC), no targeted therapy is available to treat this major breast cancer subtype. This study is aimed at identifying clinically targetable pathways that are aberrantly active downstream of E-cadherin loss in ILC.
Methods: Reverse-phase protein array (RPPA) analyses were performed in the context of E-cadherin loss using mouse and human breast cancer cells. A combination of mRNA sequencing, conditioned medium growth assays and CRISPR-Cas9 knock-out experiments were performed to identify and validate activation of oncogenic pathways in ILC.  Human ILC samples were employed to validate activation by immunohistochemistry on tissue micro-arrays. Finally, we assessed the effect of pathway inhibition using anoikis resistance and anchorage-dependent growth in vitro.
Results: We demonstrate that E-cadherin loss leads to increased activation of FAK and PI3K/AKT signalling. Autocrine activation of growth factor receptor signalling and its downstream PI3K/AKT hub was a direct consequence of E-cadherin loss, independent of activating mutations in either PIK3CA, AKT or PTEN. Analysis of human ILC samples confirmed pathway activity, and pharmacological inhibition of AKT using AZD5363 and MK2206 resulted in robust inhibition of cell growth and survival of ILC cells in anchorage-dependent and independent conditions. Moreover, our results indicate a role for intracellular FAK in the regulation of ILC anoikis resistance.
Conclusion: Our data demonstrate that E-cadherin loss evokes additional PI3K/AKT activation independent of oncogenic mutations in this pathway. We propose clinical intervention of PI3K/AKT in ILC based on functional E-cadherin inactivation, irrespective of activating pathway mutations.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Expression profiling (RNA-seq) of mouse (mILC-1, mILC-2) and human (IPH-926) invasive lobular carcinoma cell lines in adherent and suspension cell culture conditions.

first: Milou

last: Tenhagen

first: Katy

last: Teo

first: Natalie

last: ter Hoeve

first: Eric

last: Strengman

first: Adam

last: Byron

first: Ana

middle: M

last: Sotoca

first: Abhishek

middle: A

last: Singh

first: Hendrik

middle: G

last: Stunnenberg

first: Matthias

last: Christgen

first: Paul

last: van Diest

first: Valerie

last: Brunton

first: Patrick

middle: W

last: Derksen


title: Redefining the sRNA transcriptome of Streptococcus pneumoniae serotype 2 strain D39

status: Public on Mar 11 2019

city: Houston

first: Nicholas

last: De Lay

state: Texas

address: 6431 Fannin St

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center

type: Non-coding RNA profiling by high throughput sequencing

summary: Streptococcus pneumoniae (pneumococcus) is a major human respiratory pathogen and the leading cause of bacterial pneumonia worldwide. Small regulatory RNAs (sRNAs), which often act by post-transcriptionally regulating gene expression, have been shown to be crucial for the virulence of S. pneumoniae and other bacterial pathogens. Over 170 putative sRNAs have been identified in S. pneumoniae TIGR4 strain (serotype 4) through transcriptomic studies, and a subset of these sRNAs have been further implicated in regulating pneumococcal pathogenesis. However, there was little overlap in the sRNAs identified among these studies, which indicated that the approaches used for sRNA identification were not sufficiently sensitive and robust and that there were likely many more undiscovered sRNAs encoded in the S. pneumoniae genome. Here, we sought to comprehensively identify sRNAs in Avery's virulent S. pneumoniae strain D39 using two independent RNA-seq based approaches. We developed an unbiased method for identifying novel sRNAs from bacterial RNA-seq data and have further tested the specificity of our analysis program towards identifying sRNAs encoded by both strains D39 and TIGR4. Interestingly, the genes for 15% of the putative sRNAs identified in strain TIGR4 including ones previously implicated in virulence were not present in strain D39 genome suggesting that the differences in sRNA repertoires between these two serotypes may contribute to their strain-specific virulence properties. Finally, this study has identified 67 new sRNA candidates in strain D39, 28 out of which have been further validated, raising the total number of sRNAs that have been identified in strain D39 to 112.

overall_design: 6 samples;


title: Single-cell RNA sequencing of human kidney

status: Public on May 30 2019

city: Nanning

first: Zhenyuan

last: Yu

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

summary: A comprehensive cellular anatomy of normal human kidney is crucial to address the cellular origins of renal disease and renal cancer. Some kidney diseases may be cell type-specific, especially renal tubular cells. To investigate the classification and transcriptomic information of human kidney, we performed a method to obtain single-cell suspension of kidney rapidly, and conducted single-cell RNA sequencing (scRNA-seq). We present scRNA-seq data of 23,366 high quality cells from human kidneys of 3 donors. In this dataset, we show 10 clusters of normal human renal cells. Due to the high quality of single cell transcriptomic information, proximal tubule (PT) cells were classified into 3 subtypes and collecting ducts cells into 2 subtypes. Collectively, our data will provide a reliable reference for the studies of renal cell biology and kidney diseases.

overall_design:
Primary kidney samples from 3 patients were used for single cell RNA sequencing by 10X Genomics

Please note that both raw and processed data files associated with each sample have been updated on Oct 31, 2019.

first: Jinling

last: Liao

first: Yang

last: Chen

first: Chunlin

last: Zou

first: Haiying

last: Zhang

first: Jiwen

last: Cheng

first: Deyun

last: Liu

first: Tianyu

last: Li

first: Qingyun

first: Zengnan

last: Mo


title: Genome-wide profiling for h3k4me3, h3k27me3, and h3k9me3 in Uhrf1hepKO mouse livers

status: Public on Jun 06 2019

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

summary: This study was carried out to investigate potential changes in the genome-wide distribution of h3k4me3, h3k27me3, and h3k9me3 in Uhrf1hepKO mouse livers compared to wild-type.

overall_design: ChIP was carried out to pull down h3k4me3, h3k27me3, or h3k9me3 bound chromatin from nuclei isolated from wild-type and Uhrf1hepKO liver tissues. This chromatin fraction was then digested using micrococcal nuclease to release mononucleosomes. DNA fragments purified from nucleosomes were then used to generate libraries and sequenced.

first: Sadler

last: Kirsten

first: Chi

last: Sadler (Edepli)


title: LncRNA/mRNA expression profiling for human normal arterial intimae and advanced atherosclerotic plaques

status: Public on Mar 18 2019

city: Guangzhou

first: Jing-Jing

last: Zhao

state: Guangdong

address: No.1838, North of Guangzhou Avenue

institute: Laboratory Medicine Center, Nanfang Hospital, Southern Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
In microarray analysis, we have characterized the lncRNA and mRNA profiles in three advanced atherosclerosis samples and in three normal intima tissues. A total of 30,586 lncRNAs and 26,109 coding transcripts were detected by microarray analysis.
The microarray profiling analysis not only provides new insights into the pathogenesis of atherosclerosis, but may also reveal new biomarkers for its diagnosis and treatment.

overall_design: In the study presented here, 6 human samples (3 normal arterial intimae and 3 advanced atherosclerotic plaques) were used to acquire expression profiles, which provide further insight into the pathologies of atherosclerosis.

first: Yan

last: Hu


title: Identification of mesenchymal progenitors in the early limb bud

status: Public on May 16 2019

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Identification of progenitors populations through FACS in the early limb buds (E10.5 and E11.5) followed by RNA-seq. These populations showed distinct signalling pathways, that were confirmed in vitro and in vivo.

overall_design: 5 different populations were analysed in triplicates.

first: Fabiana

last: Gullotta

first: Robert

last: Reinhardt

last: Ivanek

first: Rolf

last: Zeller


title: Iron-responsive genes in Lachancea kluyveri

first: Po-Chen

last: Hsu

summary: To understand the iron-responsive gene expression in Lachancea kluyveri under high and low iron conditions, we perfomred the genome-wide gene expression profiling for the log-phase cells of Lachancea kluyveri wild type, sef1 deletion, aft1 deletion and sef1aft1 double deletion mutants under the YPD+400mM ferrous iron and YPD+ 200 mM BPS conditions.

overall_design: Cells fom overnight YPD cultures were diluted into YPD+400mM and YPD+200mM BPS at a cell density of 0.5 OD per ml and incubated at 30°C fro 5.5 h.  Four biological replicates fro each strain under each condition were preprared with an exception of sample SF, which has only three biilogical replicates.

first: Jun-Yi

last: Leu


title: Gene expression profiling of optic tectum neuroepithelial cells in adult medaka

status: Public on Apr 20 2019

city: Paris

first: Emilie

last: Dambroise

address: 24 bd Montparnasse

institute: Institut Imagine

summary: WDR12 is a ribosome biogenesis factor known to be expressed in Optic tectum Neuroepithelial cells, we define the transcriptome profile of the optic tectum neuroepithelial cells, by cell-sorting followed by RNA-seq (Illumina technology).

overall_design: Using a Neuroepithelial cells driven medaka line expressing GFP under the control of the wdr12 promoter,( a ribosome biogenesis factor known to be expressed in Optic tectum  Neuroepithelial cells, we define the transcriptome profile of the optic tectum neuroepithelial cells, by cell-sorting followed by RNA-seq(Illumina technology) of wdr12:GFP+ and wdr12:GFP- tectal cells . The wdr12:GFP- cell population is a mix of several cell types (transitory-amplifying progenitors, post-mitotic neurons and glial cells). We used, as an additional control, the ebf3:GFP line (Mongin et al., 2011), in which post-mitotic progenitors and differentiated neurons of OT are GFP-positive in one month-old medakas.

first: E

first: T

last: Bourquard

first: M

last: Simion

first: J

middle: S

last: Joly


title: RUNX1 mutations lead to a myeloid differentiation block by altering the RUNX1 transcriptional program

status: Public on Feb 06 2019

first: Joost

last: Martens

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Degenerate 3'UTR DNA and RNA sequence data

city: Seattle

first: Georg

last: Seelig

state: WA

address: 3946 W Stevens Way NE

department: Electrical Engineering

institute: University of Washington

summary: We assayed the expression of millions of alternative polyadenylation reporters constructed from randomized sequences

overall_design: Alternative polyadenylation isoforms from the variant library were quantified using RNA-Seq, mapped to their degenerate 3'UTR source plasmid, and the sequence and expression data used to train a convolutional neural network

first: Nicholas

last: Bogard

first: Johannes

last: Linder


title: RUNX1 mutations lead to a myeloid differentiation block by altering the RUNX1 transcriptional program (ChIP-Seq)

summary: Mutations in the RUNX1 gene (RUNX1mut) have been established in myelodysplasia (MDS), de novo and secondary acute myeloid leukaemia (AML), and are in general associated with an unfavourable clinical outcome. Familial RUNX1 mutations are associated with familial thrombocytopenia and these patients have a predisposition to AML development. However, a number of studies have been performed so far in mice which might be distinct from the human hematopoietic system. Therefore we studied the cellular phenotypes, the RUNX1 binding pattern and expression profile induced by RUNX1mut in cord blood (CB) CD34+ cells and induced pluripotent stem cell (iPSC) and compared these findings to primary RUNX1mut AML’s.

overall_design: A total of six samples were subject to ChIP-Seq including control and RUNX1mut-transduced groups in cord blood CD34 cells as well as time-course iPSCs.


summary: To understand the highly active Sef1-VP16 dependent gene expression in Lachancea kluyveri under both fermentative and respiratory conditions, we perfomred the genome-wide gene expression profiling for the log-phase cells of Lachancea kluyveri wild type and SEF1-VP16 gain-of-function mutant under both YPD and YPGly conditions.

overall_design: Cells fom overnight YPD cultures were diluted into YPD and YPGly at a cell density of 0.2 OD per ml and incubated at 30°C fro 5.5 h.  Four biological replicates fro each strain under each condition were preprared.


title: Next Generation Sequencing of Wild Type and Nlrp6-/- T cells

status: Public on May 08 2019

summary:
Nlrp6 is expressed by T cells, but whether Nlrp6 influences the transcriptom of T cells is not known
Methods: Equal numbers of Wild Type and Nlrp6-/- CD4 T cells were adoptively transfered in RAG-/- hosts, isolated from the colonic lamina propria and mRNA profiles gernerated by next generation squencing in quadruplicates using Illumina squencers.
Conclusions: Our study indicates that Nlrp6  may regulate genes that are involved in apoptosis of T cells

first: Jan

last: Niess

first: Julien

last: Roux


title: Transcriptomic profiles of spleen in piglets exposed to Fumonisin B1

first: Yannick

last: Lippi

summary: Fumonisin B1 (FB1) is a mycotoxin produced by Fusarium species. In mammals, this toxin causes multiple organ-specific damages. Among its multiple effects, FB1 promotes hepatotoxicity, is immunotoxic and alters the intestinal functions. Despite its inhibitory effect on de novo ceramide synthesis, the molecular mechanism of FB1 action and toxicity remain unclears. In order to explore the mechanism of FB1 toxicity, we analyzed the transcriptome of the spleen.

overall_design: Ten weeks old pigs were sacrificed after 4 weeks feeding with control diet (6 pigs) or feeding with control diet artificially contaminated with 10 ppm Fumonisin B1 (6 pigs). After sacrifice spleen samples from each of 12 pigs are collected and used for microarray gene expression study. Among 6 samples for each condition, only 5 were kept for statistical analysis after quality control analysis.

first: Nicolas

last: Loiseau

first: Pascal

last: Gourbeyre

first: Joëlle

last: Laffitte

last: Fayet

first: Anne-Marie

last: Cossalter

first: Philippe

last: Pinton

first: Isabelle

last: Oswald


title: Risk prediction models for dementia constructed by supervised principal component analysis using miRNA expression data

status: Public on Feb 26 2019

city: Obu

first: Daichi

last: Shigemizu

state: Aichi

address: 7-430 Morioka-cho

institute: National Center for Geriatrics and Gerontology

summary: Alzheimer’s disease (AD) is the most common subtype of dementia, followed by Vascular Dementia (VaD), and Dementia with Lewy Bodies (DLB). Recently, microRNAs (miRNAs) have received a lot of attention as the novel biomarkers for dementia. Here, using serum miRNA expression of 1,601 Japanese individuals, we investigated potential miRNA bio- markers and constructed risk prediction models, based on a supervised principal component analysis (PCA) logistic regression method, according to the subtype of dementia. The final risk prediction model achieved a high accuracy of 0.873 on a validation cohort in AD, when using 78 miRNAs: Accuracy = 0.836 with 86 miRNAs in VaD; Accuracy = 0.825 with 110 miRNAs in DLB. To our knowledge, this is the first report applying miRNA-based risk pre- diction models to a dementia prospective cohort. Our study demonstrates our models to be effective in prospective disease risk prediction; and with further improvement may contribute to practical clinical use in dementia.

overall_design: 1,601 serum samples (1,021 AD cases, 91 VaD cases, 169 DLB cases, 32 Mild Cognitive Impairment: MCI, and 288 NC).

first: Shintaro

last: Akiyama

first: Yuya

last: Asanomi

first: Keith

last: Boroevich

first: Alok

last: Sharma

first: Tatsuhiko

last: Tsunoda

first: Kana

last: Matsukuma

first: Makiko

last: Ichikawa

first: Hiroko

last: Sudo

first: Satoko

last: Takizawa

first: Takashi

last: Sakurai

first: Takahiro

last: Ochiya

first: Kouichi

last: Ozaki

first: Shumpei

last: Niida


title: Transcriptomic profiles of liver in piglets exposed to Fumonisin B1

first: Yannick

last: Lippi

summary: Fumonisin B1 (FB1) is a mycotoxin produced by Fusarium species. In mammals, this toxin causes multiple organ-specific damages. Among its multiple effects, FB1 promotes hepatotoxicity, is immunotoxic and alters the intestinal functions. Despite its inhibitory effect on de novo ceramide synthesis, the molecular mechanism of FB1 action and toxicity remain unclears. In order to explore the mechanism of FB1 toxicity, we analyzed the transcriptome of the liver which is targeted by FB1.

overall_design: Ten weeks old pigs were sacrificed after 4 weeks feeding with control diet (6 pigs) or feeding with control diet artificially contaminated with 10 ppm Fumonisin B1 (6 pigs). After sacrifice liver samples from each of 12 pigs are collected and used for microarray gene expression study. Among 6 FB1 treated samples, only 5 were kept for statistical analysis after quality control analysis.

first: Nicolas

last: Loiseau

first: Pascal

last: Gourbeyre

first: Joëlle

last: Laffitte

first: Julien

last: Fayet

first: Anne-Marie

last: Cossalter


title: Single-cell RNA-sequencing of mouse double-negative developing thymocytes

status: Public on Feb 04 2019

first: DBM Bioinformatics

last: Core Facility

summary: We performed a single-cell transcriptome analysis of double-negative developing thymocytes from the DN2, DN3 and DN4 populations

overall_design: Double-negative developing thymocytes from the DN2, DN3 and DN4 populations were sorted from six WT mice and used for single cell RNA Seq (10x genomics platform)

first: Fabian

last: Klein

last: Roux


title: RNA-sequencing of mouse double-negative developing thymocytes [WT and Duxbl[ind]xpTa[Cre]]

summary: We performed a transcriptome comparison of double-negative developing thymocytes from the DN3-4 population, from mice overexpressing the transcription factor Duxbl and wild type mice

overall_design: Double-negative developing thymocytes from both WT and Duxbl[ind]xpTα[Cre] mice were gated for CD4-, CD8-, CD3-, B220-, CD25int, CD44low and CD117low expression, which define the DN3-4 stage of thymocyte development. The experiment was performed in four replicates, giving a total of 8 samples.


title: Expression analysis of Lgr5 hair follicle stem cells following skin injury in the presence and absence of regulatory T cells

status: Public on Mar 31 2019

city: San Francisco

first: Anubhav

middle: N.

last: Mathur

state: California

address: 513 Parnassus Ave, HSW12

institute: University of California, San Francisco

summary: The goal of this study was to identify transcripts that were differentially regulated in Lgr5 hair follicle stem cells following skin injury in the presence and absence of regulatory T cells

overall_design: Lgr5-traced cells were isolated using flow cytometry from the epidermis of reporter mice, following skin barrier injury and in the presence or absence of Treg cells.

middle: N

first: Michael

last: Rosenblum


title: Unleashing Type-2 Dendritic Cells

status: Public on Apr 04 2019

first: Joshua

last: Pollack

state: CA

address: 2 Tower Pl.  Ste 800

institute: Pionyr Immunotherapeutics

summary: Singe-cell transcriptomic profiling of myeloid cells from mouse and human tumor-draining lymph nodes

overall_design:
10X Genomics single-cell RNA sequencing of sorted myeloid cells from mouse (WT and Foxp3DTR) and human tumor-draining lymph nodes
Sumitter's statement: Raw data (bam) for Human TDLN to be submitted.
Raw data (bam) for Mouse TDLN_FOXP3DTR filed upload due to corruption.

first: Mikhail

last: Binnewies

first: Matthew

last: Krummel


title: Transcriptome analysis of ARF and Aux/IAA expression during the induction of somatic embryogenesis in Coffea canephora

status: Public on Apr 03 2019

city: Mérida

first: Víctor M.

last: Loyola-Vargas

state: Yucatán

department: Unidad de Bioquímica y Biología Molecular de Plantas

country: Mexico

institute: Centro de Investigación Científica de Yucatán

summary: Somatic embryogenesis (SE) is a useful biotechnological tool to study the morpho-physiological, biochemical and molecular processes during the development of Coffea canephora. Plant growth regulators (PGR) play a key role during cell differentiation in SE. The Auxin-response-factor (ARF) and Auxin/Indole-3-acetic acid (Aux/IAA) are fundamental components involved in the signaling of the IAA. The IAA signaling pathway activates or represses the expression of genes responsive to auxins during the embryogenic transition of the somatic cells. The growing development of new generation sequencing technologies (NGS), as well as bioinformatics tools, has allowed us to broaden the landscape of SE study of various plant species and identify the genes directly involved. Analysis of transcriptome expression profiles of the C. canephora genome and the identification of a particular set of differentially expressed genes (DEG) during SE are described in this study. A total of eight ARF and seven Aux/IAA differentially expressed genes were identified during the different stages of the SE induction process. The quantitative expression analysis showed that ARF18 and ARF5 genes are highly expressed after 21 days of the SE induction, while Aux/IAA7 and Aux/IAA12 genes are repressed. The results of this study allow to have a better understanding of the genes involved in auxin signaling pathway as well as their expression profiles during the SE process.

overall_design: A total of 12 single-end libraries were sequenced via Illumina® NextSeqTM 500 system. Two technical sequencing replicates for each biological sample were conducted corresponding to 14, 9 and 0 days before induction (DBI), and 1, 2 and 21 days after induction (DAI). The 14 DBI sample corresponds to the control.

first: Ana

middle: O

last: Quintana-Escobar

first: Geovanny

middle: I

last: Nic-Can

first: Rosa

last: Galaz-Ávalos

first: Víctor

first: Elsa

middle: B

last: Góngora-Castillo


title: Ribosomal Proteins Regulate MHC Class I Peptide Generation for Immunosurveillance

status: Public on Jan 21 2019

city: Bethesda

first: Timothy

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

summary: The MHC class I antigen presentation system enables T cell immunosurveillance of cancers and viruses.  Rapidly degraded nascent polypeptides (DRiPs) provide many class I peptide ligands.  By knocking down each of the 80 ribosomal proteins, we identified proteins that modulate peptide generation without altering source protein expression.  We show that 60S ribosomal proteins L6 (RPL6) and RPL28, which are adjacent on the ribosome, play opposite roles in generating an influenza A virus encoded peptide.  RPL6 depletion decreases ubiquitin-dependent peptide presentation, while RPL28 depletion increases ubiquitin-dependent and -independent peptide presentation.  40S ribosomal protein S28 (RPS28) knockdown increases total peptide supply in uninfected cells by increasing DRiP synthesis from non-canonical translation of “untranslated” regions and non-AUG start codons, and sensitizes tumor cells for T cell targeting.  RPL23 knocKDut decreases overall peptide supply, impairing T cell recognition of tumor cells.  Our findings raise the possibility of modulating immunosurveillance by pharmacologically targeting ribosomes.

overall_design: HEK293-Kb cells transduced with lentiviruses to knockdown RPS28, RPLP0, RPL3, RPL6, RPL28 protein, or scrambled control.

first: Jiajie

last: Wei

first: Jonathan

last: Yewdell


title: Next Generation Sequencing Facilitates Quantitative Analysis of Macrophage (RAW264.7) with and without arctigenin treatment

status: Public on Mar 07 2019

first: Lu

last: Lu

address: No.12,Airport Road,Baiyun District

institute: Guangzhou University of Chinese Medicine

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to  explore the mechanism and target of arctigenin affecting macrophages (RAW264.7)
Methods:  Total mRNA was extracted from cells using an RNA extraction kit (Qiagen K.K., Tokyo, Japan). RNA-Seq was performed using HiSeq X Ten for next-generation sequencing by OE Biotech. Co., Ltd. (Shanghai, China). Sequenced reads were mapped to the mm9 genome using hisat2.The RNA-Seq reads that were aligned against the exon regions of genes were quantified with HTSeq-Count in the RefSeq mm9 annotation. GSEA was performed on mRNA expression datasets using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Gene signatures were considered enriched if the false discovery rate (FDR) q-values and the family-wise error rate (FWER) p-values show significant difference.
Result: The GSEA from the KEGG database indicated that AG-induced biological processes involved several inflammatory process.  GSEA methods on immunologic gene sets of Molecular Signatures Database show that the gene set of NFAT5 knockout passed the filtering criteria (p<0.01)
Conclusion:  NFAT5 was the target of arctigenin

overall_design: Macrophage (RAW264.7) with vector, with 0.5 mg/mL LPS alone or combined 1 μM arctigenin treatment.

first: Shi-Hao

last: Ni


title: RUNX1 mutations lead to a myeloid differentiation block by altering the RUNX1 transcriptional program (RNA-Seq)

first: Joost

last: Martens

overall_design: A total of nine samples were subject to RNA-Seq including RUNX1mut-transduced cord blood CD34 cells and time-course iPSCs.


title: RNA-sequencing of mouse double-negative developing thymocytes

first: DBM Bioinformatics

last: Core Facility


title: RNA-sequencing of mouse double-negative developing thymocytes [CD4-, CD8-, CD3-, B220-, CD25high, CD44low, and CD117low]

summary: We performed a transcriptome comparison of double-negative developing thymocytes from the DN3 population, differing in their CD27 and CD28 expression

overall_design: Double-negative developing thymocytes were gated for CD4-, CD8-, CD3-, B220-, CD25high, CD44low, and CD117low expression, which define the DN3 stage of thymocyte development. Within this population, cells were separated in 3 groups based on their CD27 and CD28 expression (DN3a CD27low CD28low, DN3a CD27high CD28low, and DN3b CD27high CD28high) that were pooled for bulk RNA-sequencing. The experiment was performed in four replicates, giving a total of 12 samples.

first: Fabian

last: Klein

first: Julien

last: Roux


title: Gene expression profiling of IL1b induced primary human pulmonary artery endothelial cells (HPAECs) treated with or without I-BET762

status: Public on Jan 24 2019

city: Pittsburgh

first: Vijay

last: Yechoor

state: PA

address: 200 Lothrop street,

department: Vascular Medicine Institute

institute: University of Pittsburgh

summary:
Bromodomain inhibitor is a known chemotherapeutic that has been shown by others to be effective in treating pulmonary hypertension in vivo. The role of JQ1, a bromodomain inhibitor has been reported to regulate vascular smooth muscle cell proliferation and apoptosis but its effect on endothelial cells is not known. The objective of this experiment was to determine the effect of a similar bromodomain inhibitor I-BET762 on inflammation induced endothelial dysfunction. I-BET762 was  chosen over other bromodomain inhibtors due to its favorable pharmacodynamics and pharmacokinetics in clinical trials. Interestingly, I-BET762 found to reverse various inflammation altered gene expression.
We use Affymetrix Clairom S platform to determine the whole gene expression.

overall_design: HPAECs were induced with IL-1b with or without I-BET762 and appropriate control for 48h. There were three biological replicate for each group. The groups were Unstimulated with vehicle, Unstimulated with I-BET762, IL1b with vehicle and IL1b with I-BEt762

first: Vinny

last: Negi

first: Gil

last: Speyer

first: Adam

last: Handen


title: Integrated Analysis of Population Genomics, Transcriptomics and Virulence Provides Novel Insights into Streptococcus pyogenes Pathogenesis [50 strains]

status: Public on Dec 31 2018

first: Priyanka

last: Kachroo

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

summary:
Purpose: We used GAS as a model bacterial pathogen to investigate the complex relationship between genome, transcriptome, and virulence in a large population of type emm28 strains recovered from humans over 26 years in geographically diverse locations.
Methods: We chose a subset of isolates from the sequenced population of 2,101 emm28 strains that would approximately span the genetic variation present in the entire population. Fifty emm28 strains were grown in triplicate, harvested at two time points, mid-exponential (ME) and early-stationary (ES) phases of growth, and assayed in triplicate by RNA-seq. rRNA was depleted using the Ribo-Zero rRNA removal kit for Gram-positive bacteria (Illumina) and libraries were made using the ScriptSeq complete kit for bacteria (Illumina). The cDNA libraries were prepared with indexed reverse primers from the ScriptSeq Index PCR primers kit (Illumina), and purified with AMPureXP beads (Beckman Coulter).

overall_design: RNA-seq cDNA libraries for 50 strains, in triplicate, were generated at two phases of growth, mid-exponential (ME, OD600nm=0.5) and early-stationay (ES, OD600nm=1.65).

first: James

last: Musser

first: Jesus

last: Eraso


title: Transcriptome profile in  IEC4.1 cells following Cryptosporidium parvum infection

status: Public on Dec 19 2018

city: Omaha

first: Xianming

last: Chen

state: NE

address: 2500 california plaza

institute: creighton university

summary: Cryptosporidium parvum is an important opportunistic parasite pathogen for immunocompromised individuals and a common cause of diarrhea in young children in developing countries. Infection by this parasite causes significant alterations in the gene expression profiles in infected host cells. This study aims to measure the genomic wide alterations in gene expression profiles in host intestinal epithelial cells following C. parvum infection. Mouse intestinal epithelial (IEC4.1) cells were grown to 80% confluence and exposed to C. parvum infection for 24h. Total RNA was collected for the genome-wide analysis. The Agilent SurePrint G3 mouse Gene Expression Microarray (G4852A) was used for the genome-wide analysis, which provides full coverage of genes and transcripts with the most up-to-date content, including mRNAs and lincRNAs (http://www.chem.agilent.com/store/en_US/Prod-G4852A/G4852A).

overall_design: The IEC4.1 cells  were grown to 80% confluence for two groups:  control (Group A, A1-A3) and C. parvum infection (Group B, B1-B3; cells exposed to C. parvum infection for 24h). Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.


title: Time course of mesenchymal breast cancer cells (MTΔECad) undergoing transdifferentiation into terminally differentiated adipocytes

status: Public on Jan 23 2019

summary: A high degree of cell plasticity seems to promote malignant tumour progression, and an epithelial-mesenchymal transition (EMT) is suspected to provide cancer cells with increased cell plasticity for the development of metastasis and therapy resistance. Here, we have tested whether the EMT-induced cancer cell plasticity can be therapeutically exploited and we report the efficient conversion of breast cancer cells, which have undergone an EMT, into post-mitotic adipocytes. Delineation of the molecular pathways underlying such transdifferentiation has motivated a combination therapy with a MEK inhibitor and Rosiglitazone to demonstrate the conversion of invasive cancer cells into adipocytes and the repression of primary tumor invasion and metastasis formation in mouse models of breast cancer. The results indicate the high potential to utilize the increased cell plasticity of invasive cancer cells for differentiation therapy and they raise the possibility to employ pharmacological treatments to interfere with tumor invasion and metastasis.

overall_design: Mesenchymal breast cancer cells (MTΔECad) were harvested at six different time-points during trasndifferentiation into terminally differentiated adipocytes (two biological replicates per time-point)

first: Dana

last: Ishay-Ronen

first: Maren

last: Diepenbruck

first: Marco

last: Morini

first: Robert

last: Ivanek

first: Gerhard

last: Christofori


title: Genome-wide RUNX1 binding landscape in AMLs with RUNX1 mutation

first: Joost

last: Martens

institute: Radboud University

summary: Analyses of 38 AML samples through integrated multiple epigenomic analysis exposes two major epigenetic subtypes. We found that the majority of patients in an AML subtype have molecular aberrations associated with RUNX1 and splicing factors. Despite this heterogeneity, they give rise to a comparable epigenome, suggesting a common deregulation of the epigenome. Given that differentially spliced genes could result in truncated proteins and/or reduced protein levels, we speculated that mutated RUNX1 protein might deregulate the same genes targeted by mutated spliceosome factors. To explore this option, we performed genome-wide binding analysis of RUNX1 in the RUNX1 mutant (RUNX1mt) expressing AMLs, and analyzed its relationship with previous epigenetic results in our study.

overall_design: Four AML samples carrying RUNX1 mutation were sequenced


title: Expression quantitative trait loci of primary melanocytes facilitate identification of melanoma susceptibility genes

status: Public on Jan 01 2019

city: Rockville

first: Tongwu

last: Zhang

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

summary: eQTL is a powerful method to detect genotype-expression correlation. To be able to identify the genes whose expression levels are correlated with germline genetic variants including the ones associated with melanoma, eQTL analysis was performed in 106 primary melanocyte cultrures

overall_design: To perform eQTL analysis, We obtained frozen aliquots of melanocytes isolated from foreskin of 106 healthy newborn males who are mainly of European descent following an established protocol (Halaban et al. 2000) from SPORE in Skin Cancer Specimen Resource Core at Yale University. Cells were grown in Dermal Cell Basal Medium supplemented with Melanocyte Growth Kit. DNA was extracted following the protocol described below and genotypes were detected using Illumina Infinium OmniEpress array

first: Jiyeon

last: Choi

first: Kevin

last: Brown

first: Stacie

last: Loftus

first: Bill

last: Pavan


title: Differential gene expression profiling in CD4+ T cells and CD19+ B cells between rituximab-treated complete remission (CR) and incomplete remission (IR) pemphigus patients

status: Public on Nov 30 2018

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

institute: INSERM U905

summary: To understand the molecular and immunological mechanisms of remission in pemphigus patients. Remission was evaluated 5 years after rituximab onset. PBMC were purified from pemphigus whole blood patients. CD4+ T cells and CD19+ B cells were isolated by flow cytometry. Genes differentially regulated between CR and IR both in CD4+ and CD19+ cells were identified by transcriptomic approach (whole human genome).

overall_design: One-color experiments (Cy3). In CD4+ transcriptomic analysis, 5 patients were analyzed (3 CR and 2 IR). In CD19+ transcriptomic analysis, 6 patients were analyzed (3 CR and 3 IR).

first: Fréderique

last: Caillot


title: Transcriptomic profiles of jejunal Peyer's patches in piglets exposed to Fumonisin B1

status: Public on Apr 15 2019

city: Toulouse

first: Yannick

last: Lippi

address: 180 chemin de tournefeuille

institute: INRAE

summary: Fumonisin B1 (FB1) is a mycotoxin produced by Fusarium species. In mammals, this toxin causes multiple organ-specific damages. Among its multiple effects, FB1 promotes hepatotoxicity, is immunotoxic and alters the intestinal functions. Despite its inhibitory effect on de novo ceramide synthesis, the molecular mechanism of FB1 action and toxicity remain unclears. In order to explore the mechanism of FB1 toxicity, we analyzed the transcriptome of the jejunal Peyer's patches.

overall_design: Ten weeks old pigs were sacrificed after 4 weeks feeding with control diet (6 pigs) or feeding with control diet artificially contaminated with 10 ppm Fumonisin B1 (6 pigs). After sacrifice Jejunal Peyer's Patches samples from each of 12 pigs are collected and used for microarray gene expression study.

first: Nicolas

last: Loiseau

first: Pascal

last: Gourbeyre

first: Joëlle

last: Laffitte

first: Julien

last: Fayet

first: Anne-Marie

last: Cossalter

first: Philippe

last: Pinton

first: Isabelle

last: Oswald


title: Integrated Analysis of Population Genomics, Transcriptomics and Virulence Provides Novel Insights into Streptococcus pyogenes Pathogenesis [isogenic]

first: Priyanka

last: Kachroo

summary:
Purpose: We used GAS as a model bacterial pathogen to investigate the complex relationship between genome, transcriptome, and virulence in a large population of type emm28 strains recovered from humans over 26 years in geographically diverse locations.
Methods: An isogenic mutant strain (MGAS27961-10T) with a 10-T homopolymeric tract was generated using allelic exchange. Primers were used to amplify a 2,690-bp fragment using genomic DNA of MGAS28085 an emm28 clinical isolate with the naturally occurring 10 “T” variant region. The resulting PCR product was cloned into suicide plasmid pBBL740 and transformed into the parental strain MGAS27961. RNA-seq was performed on the isogenic mutant strain MGAS27961-10T and parental strain (MGAS27961-9T). Quality of the total RNA, rRNA-depleted RNA, and cDNA libraries was evaluated with RNA Nano, RNA Pico, and DNA high-sensitivity kits (Agilent Technologies), respectively, using an Agilent 2100 Bioanalyzer. For each sample, the cDNA library concentration was measured fluorometrically with Qubit™ dsDNA HS assay kits (Invitrogen). The cDNA libraries were diluted, pooled, and sequenced with an Illumina NextSeq 500 instrument.

overall_design: RNA-seq cDNA libraries for isogenic mutant strain (MGAS27961-10T) and parental strain (MGAS27961-9T), in triplicate, were generated at two phases of growth, mid-exponential (ME, OD600nm=0.5) and early-stationay (ES, OD600nm=1.65).

first: James

last: Musser

first: Jesus

last: Eraso


title: Expression data from ORMDL3 knockdown in the A549 Human Lung Epithelial cell line

status: Public on Nov 21 2018

city: London

first: William

last: Cookson

address: Dovehouse Street

institute: Imperial College London

summary:
Asthma is characterized by intermittent inflammation of the airways, airflow limitation and wheeze. The ORMDL3 locus on chromosome 17q21 confers the major genetic susceptibility to childhood asthma. Although sphingolipids are important in immune signalling, the mechanisms of action of ORMDL3 on airway inflammation are incompletely understood.
We used Affymetrix Human Gene 1.1 ST microarrays to detail the global effects of siRNA-mediated ORMDL3 knockdown during the time course of IL1B-induced inflammation in the A549 Human Lung Epithelial cell line.

overall_design: A total of 38 samples were analyzed (19 control, 19 ORMDL3 knockdown) across 5 time-points (0, 2, 4, 8 and 10 hours following IL1B stimulation), with a minimum of 3 replicates per condition/time point combination. Differential expression was assessed in Limma (3.22.7). P-values were adjusted for multiple testing by the Benjamini and Hochberg method, controlling the expected FDR below 0.05.

first: Youming

last: Zhang

first: Saffron

last: Willis-Owen

first: Sarah

last: Spiegel

first: Clare

last: Lloyd

first: Miriam

last: Moffatt


title: Dissecting the human liver cellular landscape by single cell RNA-seq reveals novel intrahepatic monocyte/ macrophage populations

status: Public on Oct 22 2018

city: Toronto

first: Jeff

last: Liu

state: Ontario

address: 101 College Street, RM 4-601

department: Princess Margaret Cancer Center

institute: University Health Network

summary: The liver is the largest solid organ in the body and is critical for metabolic and immune functions. However, surprisingly little is known about the cells that make up the human liver and its immune microenvironment. To address this, we mapped the cellular landscape in the human liver using single cell RNA sequencing. We carefully fractionated fragile, fresh hepatic tissue from human livers to obtain viable parenchymal and non-parenchymal cells. Our single cell transcriptomics map reveals 20 discrete cell populations, including a novel description of distinct monocyte/ macrophage populations in the human liver. We present a comprehensive view of the human liver at single cell resolution that outlines new characteristics of resident cells in the liver, and in particular provides a new map of the human hepatic immune microenvironment.

overall_design: Primary liver samples from 5 patients were used for single cell RNA sequencing by 10X Genomics

first: Sonya

last: MacParland

first: Gary

middle: D

last: Bader

first: Ian

last: McGilvray


title: Integrated Analysis of Population Genomics, Transcriptomics and Virulence Provides Novel Insights into Streptococcus pyogenes Pathogenesis

city: Houston

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: Single cell RNAseq analysis of mouse AAA samples

status: Public on Nov 01 2018

city: New York

first: Michele

last: Silvestro

state: NY

address: 550 1st Avenue

department: Surgery

institute: New York University Langone Medical Center

summary: We report the application of single-cell-based RNA sequencing technology for high-throughput profiling of mice abdominal aortic aneurysm cell type dependent transcriptome. This study provides insight in the expression profile of aortic tissue macrophages in pathological conditions related to cardiovascular diseases.

overall_design: Examination of cell specific transcriptomes in three pooled AAA single cell suspensions from three pooled Apolipoprotein deficient mice perfused for 28 days with angiotensin II

first: Bhama

last: Ramkhelawon


title: Foxf2 plays a dual role during TGFb-induced EMT by promoting apoptosis yet enabling cell junction dissolution and migration.

status: Public on Oct 09 2018

first: DBM Bioinformatics

last: Core Facility

address: Hebelstrasse 20

institute: University of Basel

summary: We have identified the transcription factor forkhead box protein F2 (Foxf2) to be upregulated in its expression during the EMT process and studied its functional contribution to EMT by siRNA-mediated knockdown in NMuMG cells treated for 4 days with TGFbeta followed by mRNA-sequencing. Our analysis revealed a dual role of Foxf2 during TGFbeta-induced EMT in promoting apoptosis while inducing cell junction breakdown and migration.

overall_design: mRNA sequencing of NMuMG/E9 cells transfected with control siRNA or Foxf2 specific siRNA and treated with TGFbeta for 4 days

first: Nathalie

last: Meyer-Schaller

first: Robert

last: Ivanek

first: Gerhard

last: Christofori


title: Tissue signals imprint ILC2 identity with anticipatory function [single cell RNA-Seq]

status: Public on Sep 10 2018

first: Roberto

last: Ricardo-Gonzalez

address: 513 Parnassus Ave, HSE-1001

institute: University of California San Francisco

summary: Group 2 innate lymphoid cells (ILC2s) are distributed systemically and produce type 2 cytokines in response to a variety of stimuli, including the epithelial cytokines interleukin (IL)-25, IL-33, and thymic stromal lymphopoietin (TSLP).  Transcriptional profiling of ILC2s from different tissues, however, grouped ILC2s according to their tissue of origin, even in the setting of combined IL-25, IL-33R and TSLPR-deficiency.  Single-cell profiling confirmed a tissue-organizing transcriptome and identified ILC2 subsets expressing distinct activating receptors, including the major subset of skin ILC2s, which were activated preferentially by IL-18.  Tissue ILC2 subsets were normal in germ- free mice, suggesting that endogenous, tissue-derived, signals drive the maturation of ILC2 subsets by controlling expression of distinct patterns of activating receptors, thus anticipating tissue-specific patterns to perturbations occurring later in life.

overall_design: 8-14 week old ILC2 reporter mice were used to sort steady-state activated ILC2 from bone marrow, lung, visceral adipose tissue, small intestine lamina propia and skin.

first: Steven

last: Van Dyken

first: Richard

last: Locksley


title: Tissue signals imprint ILC2 identity with anticipatory function


title: Integrated Analysis of Population Genomics, Transcriptomics and Virulence Provides Novel Insights into Streptococcus pyogenes Pathogenesis [442 strains]

first: Priyanka

last: Kachroo

summary:
Purpose: We used GAS as a model bacterial pathogen to investigate the complex relationship between genome, transcriptome, and virulence in a large population of type emm28 strains recovered from humans over 26 years in geographically diverse locations.
Methods: We chose a subset of isolates from the sequenced population of 2,101 emm28 strains that would approximately span the genetic variation present in the entire population. 442 emm28 strains grown as singleton cultures and harvested at one time point (early-stationary phase), and libraries were prepared using RNAtag-seq. Quality of the total RNA, rRNA-depleted RNA, and cDNA libraries was evaluated with RNA Nano, RNA Pico, and DNA high-sensitivity kits (Agilent Technologies), respectively, using an Agilent 2100 Bioanalyzer. For each sample, the cDNA library concentration was measured fluorometrically with Qubit™ dsDNA HS assay kits (Invitrogen). The cDNA libraries were diluted, pooled, and sequenced with an Illumina NextSeq 500 instrument.

overall_design: We made 57 pools containing total RNA from 8 strains each, and 1 additional pool with total RNA from 5 strains. Thus, single-stranded cDNAs were organized into 58 pools. Subsequently, each set of four pools was combined into one superpool rendering 14 superpools, and one additional superpool containing only 2 pools. 15 superpools were sequenced on Illumina NextSeq 500 instrument. Demultiplexing of reads from superpools into separate pools was performed with bcl2fastq.  Read quality assessment and read quality trimming were done with FASTQC and Trimmomatic, respectively. Reads from each pool were demultiplexed into separate fastq files corresponding to individual samples based on the inline barcodes using FASTX-toolkit.

first: James

last: Musser

first: Jesus

last: Eraso


title: hESC-based human glial chimeric mice reveal glial differentiation defects in Huntington disease

status: Public on Nov 10 2018

city: Rochester

last: Goldman

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

summary: Huntington’s disease (HD) is characterized by hypomyelination as well as by neuronal loss. To assess the basis for white matter involution in HD, we generated bipotential glial progenitor cells (GPCs) from human embryonic stem cells (hESCs), derived from either huntingtin (mHTT)-mutant embryos or normal controls, and performed RNA sequence analysis to assess mHTT-dependent changes in gene expression. In hGPCs derived from 3 distinct mHTT-expressing hESC lines, a set of transcription factors associated with glial differentiation and myelin synthesis was sharply down-regulated, relative to normal hESC GPCs. In particular, NKX2.2, OLIG2, SOX10 and MYRF were all suppressed, with the consequent diminution of myelinogenesis-associated transcription. Accordingly, when mHTT-expressing hGPCs were transplanted into hypomyelinated shiverer mice, the resultant mHTT glial chimeras were hypomyelinated. The mHTT hGPCs also manifested impaired astrocytic differentiation, and developed abnormal fiber domain architecture. These data suggest that white matter involution in HD is a product of a cell-autonomous mHTT-dependent suppression of both astrocytic and oligodendrocytic differentiation by affected GPCs.

overall_design: Embryonic stem cells (hESCs) derived from 3 Huntington's disease embryos (designated to HD lines 17, 18, and 20) and 2 healthy control embryos (designated to CTR lines 02 and 19) were obtained from Genea Biocells, Sydney, Australia (http://geneabiocells.com/services/shelf-products/human-embryonic-stem-cells/). The hESC lines were differentiated into glia by previously described methods (Wang et al., 2013) and further purified by FACS targeting CD140a for enriched populations of Glial Progenitor Cells (GPCs) and CD44 for enriched populations of Astrocyte Progenitor Cells (APCs). The purified glial cell populations where then used in mRNA isolation by PolyA selection and mRNA sequencing analysis. Please note that the FASTQ files in the submission were edited by Trimmomatic. The software is used to trim adapter sequences and low-quality bases (see processing steps). The overall file structure and format remained unchanged. The count matrix in the submission is as obtained directly from featureCounts tool, that is, no manipulation was performed to the count data. The data normalization was performed internally in the analysis but the raw count data were used in differential expression analysis. Please refer to the Materials and Methods section in supplementary files. Additionally, the complete workflow, including R scripts and count matrix, was deposited to https://github.com/cbtncph/HD-Glial-Differentiation-Block-Goldman-Lab-2017.

first: Mikhail

last: Osipovitch

first: Andrea

last: Martinez

first: Adam

last: Cornwell

first: Simrat

last: Dhaliwal

first: Lisa

last: Zou

first: Devin

last: Chandler-Militello

first: Su

last: Wang

first: Xiaojie

last: Li

first: Sarah-Jehanne

last: Benraiss

last: Agate

last: Lampp

first: Abdellatif

first: Martha

last: Windrem


title: RNA sequencing of FHR1-treated human monocytes

status: Public on Aug 25 2018

city: Jena

first: Christine

last: Skerka

address: Beutenbergstraße 11A

department: Infection Biology

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

summary: The plasma protein FHR1 induces release of inflammatory cytokines IL-1β, IL-6, IL-18 or TNFα from blood-derived human monocytes. RNA sequencing was performed from RNA of BSA- or FHR1-treated monocytes from 4 different donors. In response to FHR1, 522 monocytic genes were upregulated (gene ontology enrichment analysis), including 35 inflammation related genes, e.g. TNF. Also, G protein-coupled receptors such as EMR2/ADGRE2 were upregulated in response to FHR1.

overall_design: Blood-derived monocytes were treated with BSA or FHR1, after 4h RNA was isolated. RNA of 4 donors were combined and sequenced.

first: Sarah

last: Irmscher

first: Luke

last: Halder


title: Tissue signals imprint ILC2 identity with anticipatory function [RNA-Seq]

first: Roberto

last: Ricardo-Gonzalez

overall_design: 8-14 week old male WT or TKO (triple-deficient Crlf2-/-Il25-/-Il1rl1-/-) ILC2 reporter mice were used to sort steady-state activated ILC2s from bone marrow (WT n=3; TKO n=3), fat (visceral adipose tissue; WT n=6, TKO n=4); lung (WT n=5, TKO n=5), small intestine lamina propia (WT n=6; TKO n=5) and skin ( WT n=6, TKO n=5). One of the lung TKO samples and 2 of the small intestine TKO samples failed library prep. All other samples were included in the analyses.

first: Steven

last: Van Dyken

first: Richard

last: Locksley


title: Maternal methionine supplementation alters the epigenome of the offspring [Bisulfite-Seq]

status: Public on Jul 17 2018

city: Madison

first: Francisco

last: Peñagaricano

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin-Madison

type: Methylation profiling by high throughput sequencing

summary: Maternal nutrition can induce modifications in the epigenome of the fetus, resulting in gene expression alterations and impacting future performance. Epigenetic changes are related to nutrition via the one carbon cycle, which involves aminoacid methionine. We hypothesized that an increased dietary methionine in beef cows during early gestation will impact the whole-genome DNA methylation and transcriptome of the offspring.

overall_design: Brangus-Angus crossbred cows were randomly assigned to one of two nutritional treatments during days -30 to +90 relative to the breeding season: Control Treatment (low-quality limpograss hay supplemented with molasses and urea) and Methionine Treatment (control diet supplemented with 3.7g of rumen-protected methionine per head per day). Longissimus dorsi muscle samples were collected from 10 bull calves per maternal treatment at one month of age. Muscle tissue samples were subjected to DNA extraction, library generation, and subsequent bisulfite sequencing.

first: Rocío

last: Amorín

last: Peñagaicano


title: Kinetic analysis of TGFbeta-induced EMT in NMuMG/E9 cells

status: Public on Oct 03 2018

city: Basel

first: DBM Bioinformatics

last: Core Facility

summary: To investigate the transcriptional remodelling during EMT, we treated normal murine mammary gland epithelial cells with TGFbeta for 0, 2h, 6h, 12h, 24h, 36h, 48h, 60h, 72h, 96h, 168h and 240h. Using WGCNA and pathway enrichment analysis we identified multiple gene expression modules that were enriched in general, signaling, metabolic or stuctural pathways highly relevant for EMT.

overall_design: RNA sequencing of NMuMG/E9 cells induced to undergo EMT by treatment with TGFbeta from 0-10 days.

first: Meera

last: Saxena

first: Nathalie

last: Meyer-Schaller

first: Robert

last: Ivanek

first: Gerhard

last: Christofori


title: COPD is accompanied by coordinated transcriptional perturbation in the quadriceps affecting the mitochondria and ECM

status: Public on Aug 16 2018

first: William

last: Cookson

summary:
In this experiment we catalogue transcriptional changes accompanying COPD in the quadriceps. We measure global gene transcription in the quadriceps using Affymetrix HuGene 1.1 ST arrays in an unselected cohort of 79 stable COPD patients in secondary care and 16 healthy age-and gender-matched controls.
We identified 1,826 differentially expressed transcript clusters, comprising 6 modules of co-expressed genes, which differentially associate with clinical and immunological features of COPD.

overall_design: RNA samples derived from 95 quadriceps biopsy specimens were analysed as part of this study (79 COPD, 16 healthy). Differential expression between healthy and COPD samples was estimated using Limma (3.22.7). P-values were adjusted for multiple testing using the Benjamini & Hochberg method to control the False Discovery Rate below 5%. Patterns of transcriptional co-ordination were sought amongst differentially expressed genes through Weighted Gene Co-expression Network Analysis (WGCNA).

first: Saffron

last: Willis-Owen

first: Anna

last: Thompson

first: Paul

last: Kemp

first: Michael

last: Polkey

first: Miriam

last: Moffatt

first: Samantha

last: Natanek


title: GFI1 is pivotal for AML1-ETO positive acute myeloid leukemia

status: Public on Jul 13 2018

city: Nijmegen

first: Joost

last: Martens

state: Nederland

address: Geert Grooteplein 28

summary: AML1-ETO (Acute Myeloid Leukemia 1-Eight Twenty One) caused by the translocation t(8;21)(q22;q22) is a mutated transcription factor contributing to AML development. Although associated with a favorable prognosis, half of the patients fail to achieve long-term survival. We examined the role of the transcription factor Growth factor independence 1 (GFI1) in the initiation and progression of leukemia and exploited the use of a drug targeting GFI1 expression in the context of AML1-ETO associated AML. We could show that GFI1 is required for maintenance of AML1-ETO associated leukemia and that loss of GFI1 or targeting GFI1 expression impedes leukemia initiation and progression and could be a potential new therapeutic strategy for patients failing to respond to chemotherapy.

overall_design: ChIP-seq profiling of GFI1 in human Kasumi-1 cells and of AML1-ETO in Gfi1 wt and KO mouse spleen cells

first: Amit

last: Mandoli

first: Cyrus

last: Khandanpour


title: Maternal methionine supplementation alters the epigenome of the offspring [RNA-Seq]

first: Francisco

last: Peñagaricano

overall_design: Brangus-Angus crossbred cows were randomly assigned to one of two nutritional treatments during days -30 to +90 relative to the breeding season: Control Treatment (low-quality limpograss hay supplemented with molasses and urea) and Methionine Treatment (control diet supplemented with 3.7g of rumen-protected methionine per head per day). Longissimus dorsi muscle samples were collected from 10 bull calves per maternal treatment at one month of age. Muscle tissue samples were subjected to RNA extraction, library generation, and subsequent sequencing.

last: Amorín


title: Designing a single cell RNA sequencing benchmark dataset to compare protocols and analysis methods

status: Public on Aug 20 2018

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research


title: Application of Next Generation Sequencing (RNA-seq and miRNA-seq) to study the molecular signature of Aluminium hydroxide adjuvant in ovine peripheral blood mononuclear cells (PBMCs) [miRNA-Seq]

status: Public on Oct 30 2018

city: Leioa

first: Begoña

last: Jugo

state: Basque Country

address: Sarriena auzoa s/n

department: Genetics, Physical Anthropology and Animal Physiology

country: Spain

institute: University of the Basque Country (UPV/EHU)

summary: We report the application of miRNA sequencing technology for high-throughput profiling of the aluminium hydroxide adjuvant mechanism of action in an in vivo experiment on sheep.  We mapped about 13 million sequence reads per sample to the sheep genome (build Oar3.1) and identified 95 miRNAs in the PBMCs of sheep treated with commercial vaccines or with the adjuvant alone. A total of 3, 6 and 1 differentialy expressed miRNAs were identified in the vaccine tf VS vaccine t0, adjuvant tf VS adjuvant t0 and adjuvant tf VS vaccine tf comparisons, respectively. Furthermore, miRNA target prediction was performed and it was integrated with previous RNA-seq data in the same animals to predict reliable miRNA-mRNA interactions. Previously reported miRNAs related to alterations caused by aluminium adjuvant were found differentially expressed, namely: miR-19b and miR-125b. Within the negatively correlated targets of the differentially expressed miRNAs there are factors that are clearly related with the response to stimulus, RNA binding and cellular response to DNA damage. Taken together, our analysis provides characterization of alterations in the miRNAome caused by the aluminium adjuvant and identifies some targets of the differentially expressed miRNAs which have been previously linked to the immune system. The overrepresentation of genes related to DNA damage stimulus and DNA repair in both groups may be due to miRNA-mediated regulation.

overall_design: PBMCs miRNA profiles of six age-matched Rasa sheep before and after inoculation (t0 and tf) of nine different commercial vaccines based of aluminium hydroxide (the vaccine group composed of 3 animals) or with the aluminium adjuvant alone in an equivalent dose (the adjuvant group composed of 3 animals) were generated by deep sequencing on an Illumina HiSeq2500 sequencer. In total, the study is composed of three biological replicates per group and twelve libraries were sequenced.

first: Endika

last: Varela

first: Naiara

last: Abendaño

first: Javier

last: Asín

first: Maialen

last: Sistiaga

first: Marta

last: Pérez

first: Ramsés

last: Reina

first: Damián

last: de Andrés

first: Lluís

last: Luján


title: A distinct lineage of origin reveals heterogeneity of plasmacytoid dendritic cells I

status: Public on Jun 22 2018

first: DBM Bioinformatics

last: Core Facility

summary: Plasmacytoid  dendritic cells (pDCs) are an immune subset devoted to the production of high amounts of type 1 interferons in response to viral infections. While conventional dendritic cells (cDCs) originate mostly from a common dendritic cell progenitor (CDP), pDCs have been shown to develop from both CDPs and common lymphoid progenitors (CLP). Here we found that pDCs developed predominantly from IL7R+ lymphoid progenitor cells. Expression of SiglecH and Ly6D  defined pDC lineage commitment along the lymphoid branch. Transcriptional characterization of SiglecH+Ly6D+ precursors indicated that pDC development requires high expression of the transcription factor IRF8, while pDC identity relies on TCF4. RNA sequencing of IL7R+ lymphoid and CDP-derived pDCs mirrored the heterogeneity of mature pDCs observed by single-cell analysis. Both mature pDC subsets are able to secrete type 1 interferons, but only myeloid-derived pDCs share with cDCs their ability to process and present antigen.

overall_design: Bulk RNA Seq of BM and splenic pDCs and IL7R+ LP and CDP derived pDCs was performed. Three biological replicates were used.

first: Patrick

last: Rodrigues Fernandes

first: Robert

last: Ivanek

first: Roxane

last: Tussiwand


title: SUMO-targeted ubiquitin ligases (STUbLs) reduce the toxicity and abnormal transcriptional activity associated with a mutant, aggregation-prone fragment of huntingtin

status: Public on Jun 20 2018

city: Frederick

first: Yongmei

last: Zhao

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

summary: We report that the SUMO-targeted ubiquitin ligase (STUbL) Slx5 reduces the toxicity and abnormal transcriptional activity of a mutant, aggregation-prone fragment of huntingtin (htt), the causative agent of HD. An extra copy of SLX5 specifically reduces htt aggregates in the cytosol as well as chromatin-associated htt aggregates in the nucleus. Using RNA sequencing, we identified and confirmed specific targets of mHtt's transcriptional activity that are modulated by Slx5.

overall_design: Three independent RNA-seq libraries for each of 4 samples were prepared from total RNA of GAL-NLS-25Q-GFP (+/-SLX5) or GAL-NLS-103Q-GFP (+/-SLX5) strains after galactose induction

first: Kentaro

last: Ohkuni

first: Richard

middle: E

last: Baker

first: Munira

last: Basrai

first: Oliver

last: Kerscher


title: A Unique B-cell Regulome links Notch to Downstream Oncogenic Pathways in Small B-cell Lymphoma

status: Public on Jun 03 2018

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

department: Pathology

institute: University of Michigan Medical School

summary: We perform integrative analysis of Notch-dependent transcripts, genome-wide binding of Notch transcription complex subunits, and enhancer-promoter interactions to identify direct Notch target genes, including the oncogene MYC, and validate their relevance to mantle cell lymphoma and chronic lymphocytic leukemia in vivo.

overall_design:
RNA-Seq profiling of cell lines with or without rapid Notch signaling activation, Notch-active vs. inactive CLL lymph node biopsies, and Notch inhibitor versus control treated MCL xenografts. ChIP-Seq profiling of Notch transcription factor binding and histone acetylation in cell lines and lymphoma biopsies. 4C-Seq in 12 Rec-1 cell line samples.

Please note that only tdf processed data files are avaiable for the primary human sample ChIP-Seq datasets. The corresponding sequence raw data files have been submitted to dbGaP for controlled access sharing (dbGaP accession number phs000939).

first: Jelena

last: Petrovich

first: Michael

last: Kluk

first: Bradley

last: Bernstein

first: Jon

last: Aster

first: Warren

last: Pear


title: A distinct lineage of origin reveals heterogeneity of plasmacytoid dendritic cells III

overall_design: Bulk RNA Seq was performed from sort purified DN, SP and DP lymphoid progenitors and BM pDCs of 4 individual mice


title: Heterogeneity of plasmacytoid Dendritic Cells (pDCs) is revealed by a distinct lineage of origin

overall_design: Refer to individual Series


title: A distinct lineage of origin reveals heterogeneity of plasmacytoid dendritic cells II (scRNAseq)

overall_design: BM and splenic pDCs were sorted from 3 mice and 3000 cells/sample were used for single cell RNA Seq (10x genomics)


title: In situ Hi-C profiles of human CD4+ T cells, CD8+ T cells and B cells

status: Public on May 31 2018

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

summary: Over recent decades, it has been proposed that DNA interactions between mammalian chromosomes play an important role in the regulation of gene expression and cell fate determination. To study how DNA interactions change between cell types, high throughput chromosome confirmation capture (Hi-C) profiles were collected from CD4+ T cells, CD8+ T cells and B cells from human subjects.

overall_design: In situ HiC was performed separately on three cell types (CD4+ T cells, CD8+ T cells and B cells) from two male human subjects.

first: Timothy

last: Johanson

first: Hannah

last: Coughlan

first: Rhys

last: Allan


title: Total and GC B cells with or without miR-146a

status: Public on Jun 08 2018

city: La Jolla

first: Li-Fan

last: Lu

address: 9500 Gilman Dr., NSB 5314

department: Biological Sciences

institute: University of California, San Diego

summary: To examine the impact of miR-146a on GC B cell development, transcriptomic profilings of total B cells isolated from unimmunized mice with B cell-specific deletion of miR-146a (B-KO) or GC B cells isolated from B-KO mice upon sheep red blood cell (SRBC) immunization were done.

overall_design: B cells or GC B cells isolated from mice with B cell-specific deletion of miR-146a with or without SRBC immunization

first: Sunglim

last: Cho

first: Hyang-Mi

last: Lee

first: I-Shing

last: Yu

first: Youn

last: Choi

first: Hsi-Yuan

last: Huang

first: Somaye

last: Hashemifar

first: Ling-Li

last: Lin

first: Mei-Chi

last: Chen

first: Nikita

last: Afanasiev

first: Aly

last: Khan

first: Shu-Wha

first: Alexander

middle: Y

last: Rudensky

first: Shane

last: Crotty


title: Revealing parallel host-pathogen transcriptional dynamics using sorted subpopulations and single, Candida albicans infected macrophages

status: Public on Mar 12 2018

city: cambridge

first: Toni

middle: Marie

last: Delorey

state: ma

address: 415 main street

institute: Broad Institute

summary:
Purpose: The purpose of this study was to simulataneously examine the host and fungal pathogen transcriptional profiles of four distinct infection fates during macrophage and Candida albicans interactions
Methods: Membrane stained (Deep Red),primary, bone marrow derived, murine macrophages and Candida albicans expressing GFP and mCherry were exposed to each other over a four hour time course. Samples were collected at 0, 1, 2 and 4 hours and sorted for four infection subpopulations: 1. Macrophages which phagocytosed live C. albicans  (GFP+ /mCherry+ /Deep Red +), 2. Macrophages which phagocytosed dead C. albicans  (GFP- /mCherry+ /Deep Red +), 3. Uninfected macrophages(GFP- /mCherry- /Deep Red +) and 4. Unengulfed C. albicans (GFP+ /mCherry + /Deep Red -). Unexposed controls were also collected for some time points (i.e. macrophages never exposed to C. albicans and C. albicans never exposed to macrophages). Single macrophages infected with live or dead C. albicans were also sorted. Smart-seq2 was used to create libraries for both infection subpopulation and single, infected cell samples that were sequenced on Illumina’s Miseqand Nextseq. Basic quality assessment of Illumina reads and sample demultiplexing was done with Picard version 1.107 and Trimmomatic. Samples profiling exclusively the mouse transcriptional response were aligned to the mouse transcriptome generated from the v. Dec. 2011 GRCm38/mm10 and a collection of mouse rRNA sequences from the UCSC genome website. Samples profiling exclusively the yeast transcriptional response were aligned to the C. albicans transcriptome strain SC5314 version A21-s02-m09-r10 downloaded from Candida Genome Database. Samples containing both macrophages and C. albicans were aligned to a “composite transcriptome” made by combining the mouse transcriptome and C. albicans transcriptomes described above and alignment was done via BWA (version 0.7.10-r789.) Multi-reads (reads that aligned to both host and pathogen transcripts) were discarded. Then, each host or pathogen sample file were aligned to its corresponding reference using Bowtie2 and RSEM (v.1.2.21). Transcript abundance was estimated using transcripts per million (TPM). For subpopulation samples, TPM was calculated using edgeR, all as implemented in the Trinity package version 2.1.. Genes were considered differentially expressed only if they had a 4-fold change difference (> 4 FC) in TPM values and a false discovery rate below or equal to 0.001 (FDR < 0.001), unless specified otherwise.  For single macrophages infected with C. albicans, samples were aligned to the combined transcriptome as described above and RSEM was used to calculate TPM.
Results:  We were able to simultaneously measure the host and fungal pathogen transcriptional profiles of four distinct infection fates during macrophage and Candida albicans interactions
Conclusions: Our study represents an analysis of both distinct infection populations of macrophages and fungus.

sample_organism:
Candida albicans
Mus musculus

platform_organism:
Candida albicans
Mus musculus

overall_design: stained, primary, bone derived macrophages were exposed to GFP and mCherry expressing C. albicans. Four distinct subpopulations were collected at 0, 1, 2 and 4 hours and gene expression was measured. Single macrophages infected with Candida albicans were also collected and gene expression was measured at 2 and 4 hours

first: José

middle: F

last: Muñoz

first: Christopher

last: Ford

first: Bi

last: Li

first: Dawn

last: Thompson

first: Reeta

middle: P

last: Rao

first: Christina

last: Cuomo


title: Transcription (co)factor and miRNA regulatory landscape of EMT

status: Public on Jun 05 2018

first: DBM Bioinformatics

last: Core Facility

state: BS

department: Departement of Biomedicine

summary: This SuperSeries is composed of the SubSeries listed below.


title: Genome-wide association study and transcriptome analysis provide new insights into the white/red earlobe color formation in chicken

status: Public on May 05 2018

city: Guangzhou

first: Wei

last: Luo

state: Guangdong

address: Wushan Road

department: The College of Animal Science

institute: South China Agricultural University

type: Genome variation profiling by high throughput sequencing

summary: Background: Earlobe color is a typical external trait in chicken. There are some previous studies showing that the chicken white/red earlobe color is a polygenic and sex-linked trait in some breeds, but its molecular genetic and histological mechanisms still remain unclear. Methods: We herein utilized histological section, genome-wide association study (GWAS) and RNA-seq, further to investigate the potential histological and molecular genetic mechanisms of white/red earlobe formation in Qiangyuan Partridge chicken (QYP). Results: through histological section analysis, we found the dermal papillary layer of red earlobes had many more blood vessels than that of white earlobes. And we identified a total of 44 SNPs from Chromosome 1, 2, 3, 4, 9, 10, 11, 13, 19, 20, 23 and Z, that was significantly associated with the chicken white/red earlobe color from GWAS, along with 73 significantly associated genes obtained (e.g., PIK3CB, B4GALT1 and TP63), supporting the fact that the white/red earlobe color was also polygenic and sex-linked in QYP. Importantly, PIK3CB and B4GALT1 are both involved in the biological process of angiogenesis, which may directly give rise to the chicken white earlobe formation through regulating blood vessel density in chicken earlobe. Additionally, through contrast of RNA-seq profiles between white earlobe skins and red earlobe skins, we further identified TP63 and CDH1 differentially expressed. Combined with the existing knowledge of TP63 in epithelial development and tumor angiogenesis, we propose that down-regulated TP63 in white earlobes may play roles in thickening the skin and decreasing the vessel numbers in dermal papillary layer, thereby contributing to the white earlobe formation via paling the redness of the skin in QYP, but the specific mechanism remains further clarified. Conclusion: our findings advance the existing understanding of the white earlobe formation, as well as provide new clues to understand the molecular mechanism of chicken white/red earlobe color formation.

overall_design: 100 QYPs with white earlobe and 100 QYPs with red earlobe were separately genotyped for GWAS. Genotyping strategy was based on Specific-Locus Amplified Fragment Sequencing. GWAS was based on Plink case-control model.

first: Jiguo

last: Xu


title: Lipid addiction via Fatty Acid Synthase activates PI3K signaling in B cell non-Hodgkin’s Lymphoma (bNHL)

status: Public on Feb 01 2018

city: Mountain View

first: Afshin

last: Beheshti

address: Moffett Blvd

institute: NASA Ames Research Center